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- PDB-7c7e: Crystal structure of C terminal domain of Escherichia coli DgoR -

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Basic information

Entry
Database: PDB / ID: 7c7e
TitleCrystal structure of C terminal domain of Escherichia coli DgoR
ComponentsPutative DNA-binding transcriptional regulator
KeywordsDNA BINDING PROTEIN / D-galactonate / GntR superfamily / transcription repressor
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Putative DNA-binding transcriptional regulator
Similarity search - Component
Biological speciesEscherichia coli O7:K1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.047 Å
AuthorsLin, W.
CitationJournal: Front Microbiol / Year: 2020
Title: Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket.
Authors: Lin, Z. / Sun, Y. / Liu, Y. / Tong, S. / Shang, Z. / Cai, Y. / Lin, W.
History
DepositionMay 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative DNA-binding transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7974
Polymers26,4861
Non-polymers3123
Water57632
1
A: Putative DNA-binding transcriptional regulator
hetero molecules

A: Putative DNA-binding transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5958
Polymers52,9722
Non-polymers6236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area3060 Å2
ΔGint-111 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.037, 85.037, 111.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Putative DNA-binding transcriptional regulator


Mass: 26485.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O7:K1 (strain IAI39 / ExPEC) (bacteria)
Gene: dgoR, ECIAI39_4297
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H3MRW3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 5% PEG 400, 100mM Sodium acetate pH 5.5, 2M Lithium sulfate, 100mM Magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→73.65 Å / Num. obs: 15623 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.015 / Rrim(I) all: 0.093 / Net I/σ(I): 34.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.118.41.2432087311320.7830.2951.2782.4100
9.17-73.6523.70.047558823610.0090.04877.799.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.047→28.01 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 791 5.15 %
Rwork0.2259 25887 -
obs0.227 15020 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.31 Å2 / Biso mean: 54.1432 Å2 / Biso min: 25.92 Å2
Refinement stepCycle: final / Resolution: 2.047→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 16 32 1157
Biso mean--56.15 55.22 -
Num. residues----142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.047-2.11960.33511180.2969184568
2.1196-2.20450.30811280.25992721100
2.2045-2.30480.31371470.2601243690
2.3048-2.42620.29621110.24732726100
2.4262-2.57810.29941560.24182695100
2.5781-2.7770.27451590.23562687100
2.777-3.05620.27171380.252716100
3.0562-3.49770.22951410.23542700100
3.4977-4.40390.21791490.19512708100
4.4039-28.010.21541590.2153265398

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